Epigenetics Boot Camp: Planning and Analyzing DNA Methylation Studies

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Most recent Boot Camp: June 21-22, 2018 


The Epigenetics Boot Camp is a two-day intensive boot camp of seminars and hands-on analytical sessions to provide an overview of concepts, techniques, and data analysis methods utilized in human epigenetics studies.       



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boot camp overview

Summer 2018 dates: June 21-22, 2018; 8:00am - 5:30pm

Summer 2019 dates: TBD

This two-day intensive boot camp integrates the principle concepts of epigenetics and the effects of risk factors on the epigenome as we step through the key components of designing and executing DNA methylation studies. Led by a team of scientists with more than 36 years of combined expertise in the field of environmental epigenetics, the workshop will integrate seminar lectures with hands-on computer sessions to put concepts into practice. Emphasis will be given to leveraging existing resources from ongoing studies and initiating new investigations. The afternoon lab sessions will provide an opportunity to work hands-on with real methylation data generated by the Illumina Infinium MethylationEPIC (850k) BeadChip platform. Participants will learn and practice data handling, cleaning, and basic analysis of epigenome-wide DNA methylation data.

By the end of the workshop, participants will be familiar with the following topics:

  • Principles of epigenetics
  • Concept ideation and study design
  • Sample collection and processing
  • Laboratory methods and platforms for analysis
  • Data handling and cleaning
  • Data analysis
  • Study design advantages and pitfalls
  • Emerging epigenetic topics and laboratory platforms

Investigators at all career stages are welcome to attend, and we particularly encourage trainees and early-stage investigators to participate.

Prerequisites and requirements

  1. Each participant is required to bring a personal laptop as all lab sessions will be done on your personal laptop. Tablets and ipads will not work with the platform being used.

  2. The Boot Camp will use data sets in R, therefore we strongly recommend that participants have a basic understanding of this platform prior to attending the Boot Camp. It is ok if you have never used this platform before because the tutorials outlined below will provide you with the basic skills needed for Boot Camp success.

R Tutorials

Knowing basic R platform and commands are highly recommended for the Boot Camp as noted in prerequisites above. If you are new to R or need a refresher, you can review the below tutorials to be well prepared:

If you have any specific questions about R and R studio in the context of the Epigenetics Boot Camp, please email us.


The Epigenetics Boot Camp will take place on the Columbia University Medical Campus (CUMC) in New York City, specifically at Columbia Mailman School of Public Health, 722 W. 168th Street, Allan Rosenfield Building 8th Floor Auditorium. Please note that the entrance to the building is on the 10th floor (training is located two floors below entrance).

General transportation and lodging information can be found in the Getting Around section of the Training Workshops page. A PDF map of the 2018 Boot Camp location on the CUMC campus can be found here. 


John Greally, DMed, PhD, Center for Epigenomics, Albert Einstein College of Medicine. John Greally is a Professor of Genetics, Pediatrics and Medicine at the Albert Einstein College of Medicine. He received his honours degree in Medicine from the National University of Ireland in Galway (NUIG) in 1988, subsequently training in pediatrics at the Children’s Hospital of Pittsburgh and Clinical Genetics at Yale University. He received his PhD degree in 1999 and his DMed degree in 2016 from NUIG. He is the founding director of the Einstein Center for Epigenomics. His research is focused on the molecular mechanisms of human disease.


Andrea Baccarelli, MD, MPH, PhD, Mailman School of Public Health, Columbia University 

Kasey Brennan, Mailman School of Public Health, Columbia University

Andres Cardenas, PhD, Harvard Pilgrim Health Care Institute and Harvard Medical School

Elena Colicino, PhD, Icahn School of Medicine at Mount Sinai

Jonathan Heiss, PhD, Icahn School of Medicine at Mount Sinai

Allan Just, PhD, Icahn School of Medicine at Mount Sinai

Learn more about each instructor here.

Former Keynote Speakers and Instructors

Chris Mason, PhD, Weill Cornell Medical College. Keynote Speaker - August, 2017.

John Greally, DMed, PhD, Center for Epigenomics, Albert Einstein College of Medicine. Keynote Speaker - June 2017.

Cavin Ward-Caviness, PhD, Environmental Public Health Division, US Environmental Protection Agency. Instructor - June 2017.



 Early-Bird RateRegular RateColumbia Discount*
Student/Postdoc/Academic Staff      

*Columbia Discount: This discount is valid for any student, postdoc, staff, or faculty at Columbia University that pays internally through ARC rather than RegFox. To access Columbia discount, email Columbia.EBC@gmail.com for instructions.

Registration Fee: includes course material, breakfast, lunch, and refreshment breaks. Course material will be available to all students after the workshop. Lodging and transportation are not included.  

Cancellations: Cancellation notices must be received in writing one month prior to the workshop start date in order to receive a full refund. Due to workshop capacity, we regret that we are unable to refund fees for cancellations after these dates. Please email your cancellation notice to Columbia.EBC@gmail.com.


The level of knowledge and experience as well as careful planning by all instructors made the entire two-day experience worthwhile. Best applied training I have been to, I now feel equipped to work with my own data and collaborate with bioinformatics colleagues in cleaning and analyzing our data.​Dr. Kristen M., Faculty Member at University of Wisconsin-Madison, 2017 

Overall, I found the Epigenetics Boot Camp to be a very useful and comprehensive tool for learning basic principles surrounding DNA methylation analysis and interpretation. It provided a good foundation from which to build upon as I advance my knowledge in this field. - Postdoc at Emory University, 2017

I feel like I was catapulted to the forefront of the field of epigenetics for a stunning view of where the field is going. The workshop gave me clear tools and a roadmap of how to follow the brilliant minds who are leading the way. - Postdoc at Columbia University Medical Center, 2018

The Boot Camp gives a very comprehensive overview of the epigenetic research with enough technical details that all levels of participants will find informative and educational. I especially appreciate how knowledgeable the speakers are. Thank you for putting such a great workshop together! - Staff Member at Harvard University, 2017 

The Epigenetics Boot Camp was an inspiring and very helpful introduction enabling me to grasp the basics of both planning and analyzing epigenetic data. Because of the excellent instructors, one-to-one attention, and clear materials for the lectures and data-labs it was a brilliant learning experience. I would definitely recommend the epigenetics Boot Camp for anyone starting in the field of epigenetics! - Elize V., Student at Erasmus Medical Center, Rotterdam, the Netherlands, 2017  

As someone new to epigenetics, this workshop provided a great introduction to key concepts and strategies that will allow me to effectively implement epigenetic data into my research. - Student at Virginia Commonwealth University, 2018

The Boot Camp offers a great balance of introductory concepts in epigenetics with detailed strategies in data analysis. The presentation content is well organized, and the tools provided by the course are practical and helpful to conduct epigenetic studies, even for those new to epigenetics.- Lisa S., Faculty Member at Emory University, 2017

This was a very useful, all-encompassing dive into the epidemiologic methods required for epigenome-wide DNA methylation analyses.  The instruction was high-quality, and there was a strong lab component that supported application of skills to real-world data.  I would only hope for a part 2 to this quick course. - Alonzo F., Faculty Member at Cincinnati Children's Hospital Medical Center  

Additional information



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Questions? Email the Boot Camp team here.

The Epigenetics Boot Camp is hosted by Columbia University's Department of Environmental Health Sciences in the Mailman School of Public Health with additional support from Illumina, Inc.